I compile boost with both mingw (64 bit) and msvc 2013 pro. I have never in my life used the vs command prompt to build boost with msvc. Here are my commands to build 64 bit binaries on both toolchains.
First go into the boost folder and just double click bootstrap.bat. This should run and build bjam/b2. Nothing special required and doesn't matter what compiler this gets built with.
Then simply run, in a normal command prompt:
bjam.exe -a -j8 --toolset=msvc --layout=system optimization=speed link=shared threading=multi address-model=64 --stagedir=stage\MSVC-X64 release stage
Where -a forces rebuild all, -j8 means for the build to use 8 cores (adjust this based on your processor capabilities), toolset is obvious, layout means how to structure the naming of the output files, address-model is obvious, stagedir is where to output the built binaries (either relative or absolute path) and release stage is the type of build the system. See more here.
Same thing but using 64 bit mingw.
bjam.exe -j8 --toolset=gcc --layout=system optimization=speed link=shared threading=multi address-model=64 --stagedir=stage\x64 release stage
You can even go on to build additional libraries with a second pass tweaking your arguments. For example, after I've built the core libs with the above command, I run the following command to build in zlib and gzip support.
bjam.exe -a -j8 --toolset=msvc --layout=system optimization=speed link=shared threading=multi address-model=64 --stagedir=stage\MSVC-X64 --with-iostreams -s BZIP2_SOURCE=C:\dev\libraries\cpp\bzip2-1.0.6 -s ZLIB_SOURCE=C:\dev\libraries\cpp\zlib-1.2.8 release stage
Anyway that's just as an example. I linked to the full docs for the build system. Try building using these commands NOT inside a vs command prompt. If you still have problems then please post specific errors.
A note about MSVC
So, msvc compiler + boost supports a type of linking where it will automatically include additional libraries that it knows it needs. I believe boost does this by using the #pragma directive in headers. For example you might use boost::asio configured in such a way that it needs boost::system (for error codes and such). Even if you don't explicitly add boost::system library to the linker options, msvc will "figure out" that it needs this library and automatically try to link against it.
Now an issue arises here because you're using layout=system. The libraries are named simply "boost_" + the lib name, like "boost_system.dll". However, unless you specify a preprocessor define, this auto linking will try and link to a name like "boost_system_msvc_mt_1_58.lib". That's not exact as I can't recall the exact name, but you get the idea. You specifically told boost to name your libraries with the system layout (boost_thread, boost_system) etc instead of the default, which includes the boost version, "MT" if multithreaded, the compiler version, and lots of other stuff in the name. So that's why the auto linking feature goes looking for such a crazy weird name and fails. To fix this, add "BOOST_AUTO_LINK_NOMANGLE" in the Preprocessor section of your C++ settings in visual studio.
More on that here. Note that the answer here gives you a different preprocessor definition to solve this problem. I believe I ended up using BOOST_AUTO_LINK_NOMANGLE instead (which ended up working for me) because the ALL_DYN_LINK macro turned out to be designed as an "internal" define that boost controls and sets itself. Not sure as it's been some time since I had this issue, but the define I provide seems to solve the same root issue anyway.
